[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556304 sequences (80000232 bp)...
[M::process] read 556092 sequences (80000260 bp)...
[M::mem_process_seqs] Processed 556304 reads in 160.006 CPU sec, 19.930 real sec
[M::process] read 555924 sequences (80000264 bp)...
[M::mem_process_seqs] Processed 556092 reads in 168.020 CPU sec, 20.659 real sec
[M::process] read 555910 sequences (80000153 bp)...
[M::mem_process_seqs] Processed 555924 reads in 171.753 CPU sec, 21.098 real sec
[M::process] read 556004 sequences (80000181 bp)...
[M::mem_process_seqs] Processed 555910 reads in 171.456 CPU sec, 21.017 real sec
[M::process] read 555962 sequences (80000217 bp)...
[M::mem_process_seqs] Processed 556004 reads in 168.607 CPU sec, 20.702 real sec
[M::process] read 555856 sequences (80000237 bp)...
[M::mem_process_seqs] Processed 555962 reads in 174.241 CPU sec, 21.380 real sec
[M::process] read 555846 sequences (80000281 bp)...
[M::mem_process_seqs] Processed 555856 reads in 173.949 CPU sec, 21.365 real sec
[M::process] read 398474 sequences (57351937 bp)...
[M::mem_process_seqs] Processed 555846 reads in 169.594 CPU sec, 20.845 real sec
[M::mem_process_seqs] Processed 398474 reads in 123.135 CPU sec, 15.171 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -L 20,5 -t 8 -a -M -T 10 -A 1 -B 4 -O 6 -R @RG\tID:PortGambleWA_FG191\tSM:PortGambleWA_FG191\tPL:Illumina reference.fasta PortGambleWA_FG191.R1.fq.gz
[main] Real time: 186.853 sec; CPU: 1483.443 sec